SNPMiner Trials by Shray Alag


SNPMiner Trials: Clinical Trial Report


Report for Clinical Trial NCT00017732

Developed by Shray Alag, 2019.
SNP Clinical Trial Gene

Carrier Frequency and Incidence of Smith-Lemli-Opitz Syndrome in African Americans

RSH/Smith-Lemli-Opitz syndrome (SLOS) is one that causes mental retardation. It is common in the Caucasian population but rare in African American and African black populations. It has been shown that SLOS is caused by a specific defect in DHCR7, an enzyme used in cholesterol metabolism. Studies have already been done to determine the frequency of the SLOS-causing mutations in various geographic Caucasian populations. This study will investigate the frequency of the DHCR7 mutations in the African American population. If the frequency observed suggests that SLOS cases are not being identified in this ethnic group, the study will provide the rationale for future studies to identify these patients. The sample size will be 1,600. The study population will consist of archived biological specimens in the form of newborn screening blood spots from two newborn screening centers, one in Maryland and one in Pennsylvania. Subjects will be of African American ethnicity, including blacks of African, Caribbean, and Central American descent. Genomic DNA will be extracted from blood spots and screened for the six common SLOS mutations. If SLOS syndrome is found, followup will be attempted for the Maryland samples (the Pennsylvania samples will be totally anonymous).

NCT00017732 Smith-Lemli-Opitz Syndrome
MeSH: Syndrome Cleft Palate Hypertelorism Hypospadias Genetic Diseases, X-Linked Smith-Lemli-Opitz Syndrome
HPO: Cleft palate Hypertelorism



There are 4 SNPs

SNPs


1 R352W

In these Caucasian populations, the most common mutations (IVS8-1G>C, W151X, V326L, R352W, R404C and T93M) account for 60% of SLOS mutant alleles. --- V326L --- --- R352W ---


2 R404C

In these Caucasian populations, the most common mutations (IVS8-1G>C, W151X, V326L, R352W, R404C and T93M) account for 60% of SLOS mutant alleles. --- V326L --- --- R352W --- --- R404C ---


3 T93M

In these Caucasian populations, the most common mutations (IVS8-1G>C, W151X, V326L, R352W, R404C and T93M) account for 60% of SLOS mutant alleles. --- V326L --- --- R352W --- --- R404C --- --- T93M ---


4 V326L

In these Caucasian populations, the most common mutations (IVS8-1G>C, W151X, V326L, R352W, R404C and T93M) account for 60% of SLOS mutant alleles. --- V326L ---



HPO Nodes


HPO:
Cleft palate
Genes 457
MKKS PIGN TSR2 TMEM67 RPL26 RPL27 ASXL1 B4GALT7 RPL35A DGCR6 SF3B4 AMER1 BRIP1 ERCC4 ERCC5 PGAP3 PDE6D ESS2 ZMPSTE24 CENPF SCARF2 ORC6 USP9X RBM10 SMC1A RPS7 GDF6 TMEM216 ACTB RPS10 RPS15A PEX7 ACTG2 RPS17 RPS19 KLHL41 RPS23 RPS24 RPS26 RPS27 RXYLT1 WNT4 EYA1 RPS28 RPS29 RREB1 ARID1A CHN1 SLC10A7 TRIP13 KCNK9 CHRNA1 MEIS2 PGM1 HNRNPK CHRND TBC1D24 CHRNG HIRA RNU4ATAC TWIST1 CDC45 MEOX1 EFTUD2 FANCA HOXA2 FANCC FANCD2 GREB1L FANCE SEMA3A SLC2A10 FANCB FANCF COLEC11 FANCG UBB ARID1B MBTPS2 COG1 HOXD13 ARHGAP31 FKTN YAP1 SUMO1 HS6ST1 RECQL4 MID1 UFD1 GPC4 WDR35 FGD1 CC2D2A KMT2A FGF8 FGF9 ECEL1 FGFR1 PLCB4 FGFR3 FGFR2 DGCR8 FLRT3 MAD2L2 FTO TMCO1 POMK GMPPB KDM6A NIPBL SEC23A CHST3 FOXC2 COL2A1 FOXE1 ALX3 COL4A1 POMT2 PROK2 FLII HSPG2 FLNA FLNB PIGL PSAT1 COL9A1 FRAS1 COL9A2 COL9A3 PRRX1 COL11A1 COL11A2 TBX4 CCDC22 DEAF1 DONSON POLR1A COMT OFD1 TAPT1 FKRP WHCR NSD2 HYAL1 NELFA INPP5E WNT3 WNT5A WNT7A B3GALNT2 CEP290 POLR1C TUBB ITGA8 SHH POMGNT1 CHSY1 PORCN POU1F1 ICK CHD7 ZSWIM6 COLEC10 POMT1 TMEM107 XRCC2 SIX1 SIX3 FANCM PIGV GDF3 CCDC141 SH2B1 ARCN1 CRKL STAMBP ZIC2 EPG5 MSX1 MSX2 IGBP1 C2CD3 PIEZO2 PPP3CA NSMF KANSL1 SEC24C UBE2T G6PC3 ARVCF WDR11 CTCF FEZF1 TP63 DLL3 CEP41 PTCH2 ANKRD11 B9D1 SMARCA4 SMARCB1 SMARCC2 SIX5 SMARCE1 CTBP1 SMS MESP2 SELENOI MAPK1 CTNND1 TBR1 GRHL3 SUFU MAP2K1 IL17RD SNRPB MAP2K2 CEP57 FZD2 MCTP2 STAG2 SLX4 MUSK MEGF10 RAI1 PROP1 SEMA3E SON SOX2 SOX3 SOX9 SOX10 SOX11 TCTN3 MYH3 ATP6V1B2 KIF1BP INTU MASP1 DDX59 AHI1 ATR CHST14 TMEM237 EARS2 MYOD1 EIF4A3 RIPPLY2 SEPTIN9 INPPL1 IQSEC2 STAC3 KIAA0586 GAS1 HDAC8 PTDSS1 GATA1 CPLX1 GATA3 DAG1 FGFRL1 NFASC NBN IRF6 PLXND1 COL25A1 PHF8 SMOC1 DCC NEB PTCH1 BCOR BCR ADA2 NSUN2 ZEB2 PHGDH HESX1 B3GAT3 FGF17 DDX3X STAT3 MKS1 KIAA0753 SLC35D1 XYLT1 GJA1 BMP4 NEK1 FAM20C IMPAD1 GJB2 ZNF469 ANOS1 PTPN11 KISS1R TXNL4A CEP120 GPC3 BRCA1 BRAF BRCA2 PROKR2 KLHL7 WASHC5 FGF20 KCNH1 KCNJ2 GLI2 GLI3 PGAP2 DHCR7 DHCR24 HES7 NECTIN1 BUB1 ARNT2 DHODH CYP26C1 BUB1B PEX2 MYMK PEX5 HYLS1 MAFB KIAA0556 TAC3 RBM8A DLX4 GNAI3 CDT1 TACR3 BMPER AMMECR1 GNB1 TMEM231 FOXH1 CPLANE1 MAP3K7 MAPRE2 KISS1 NODAL GNRH1 GNRHR MED12 PIGO TBX1 NOTCH2 CDON FKBP14 GP1BB RAD21 TBX2 TBX6 RAD51 TBX22 RAD51C TBX15 NPHP1 KRAS RPGRIP1 DGCR2 VAX1 RAP1A SATB2 RAP1B B3GLCT RAPSN RPGRIP1L LHX4 NEDD4L B4GAT1 NUP107 RB1 TCOF1 DYNC2H1 SLC26A2 SMCHD1 DOK7 DUSP6 KAT6A DVL1 NUP88 DVL3 B3GALT6 CRPPA FANCL RIPK4 TDGF1 SPECC1L DPF2 LBR RET RUNX2 REV3L DLL1 PRDM5 PQBP1 TFAP2A GMNN JMJD1C WDPCP PALB2 EDN1 LETM1 LFNG EDNRA RFWD3 POLR3A KIF7 CEP55 ESCO2 TGFB3 ORC1 TGFBR1 ORC4 TGFBR2 B9D2 POLR1D TGIF1 LIG4 KMT2D OTX2 EFNB1 ALX1 POMGNT2 LMNA SMC3 SETD5 LMX1B FANCI EIF2S3 ARID2 SPRY4 TGDS MED25 HAAO TRPV4 PAX3 RPL35 CDC6 BUB3 SLC25A19 KAT6B CDH1 CSPP1 RPL5 CDH11 CD96 DISP1 RPL11 SMAD3 SMAD4 RPL15 TCTN2 RPL18 LARGE1
Hypertelorism
Genes 562
TPM2 TPM3 PIGN TMEM67 ASXL1 CTU2 SLC29A3 ERCC2 B4GALT7 RPL35A AMER1 ERCC3 BRIP1 LZTR1 ERCC4 PDE4D IRX5 PGAP3 PDE6D ERF ZMPSTE24 KREMEN1 CENPF LEMD3 MAT2A RBM10 SMC1A ACOX1 RPS6KA3 APC2 RPS7 ACTA1 ACTA2 TMEM216 ACTB PEPD BLNK PEX1 PEX6 ACTG1 DNAJC21 LAGE3 RPS19 CHD3 CHD4 KLHL41 EXT2 EXTL3 VSX1 RRAS ACY1 RREB1 EZH2 TRIP12 TRIP4 CHRNA1 MEF2C ALX4 IFT43 GATAD2B CHRNA7 HNRNPH2 RYR1 CHRND HNRNPU TBC1D24 CHRNG WAC HIRA RNU4ATAC TWIST1 SNAP29 FANCA FANCC FANCD2 GREB1L FANCE ADK SHROOM4 SLC2A10 BPTF FANCB FANCF COLEC11 FANCG ARID1B FBN1 PIGA NALCN COG1 PIK3CA STRADA AGA PIK3R1 PIK3R2 HS6ST1 JAG1 RECQL4 MID1 UFD1 A2ML1 HACE1 PITX2 GPC4 HRAS WDR35 KIAA1109 FGD1 GTF2H5 FGF3 CC2D2A ANTXR1 KMT2A ALG8 UMPS FGF8 AKT1 FGF10 FGFR1 FGFR3 FGFR2 MMP2 MAD2L2 TP53RK FH HSD17B4 TMCO1 DOCK6 ZBTB18 LTBP4 ALDH6A1 EIF2AK3 MOCS1 MOCS2 SEC23A DSE CNTN1 FOXC1 CHST3 COL1A1 FOXE3 PMM2 COL1A2 COL2A1 ALX3 COL3A1 PROK2 SLC25A24 COL5A1 FLI1 FLII HSPG2 FLNA FLNB PIGL PSAT1 EXOSC9 FRAS1 SET FBLN5 COL11A1 COL11A2 TBX4 CCDC22 OGT DEAF1 POLR1A ANK1 POC1A COMT OFD1 TAPT1 ADAMTS3 WHCR NSD2 NELFA WNT5A COL27A1 PEX3 EFEMP2 CEP290 POLR1C TUBB APC ITGA8 COX7B POR CHSY1 FBXO11 CHD7 SIN3A ZSWIM6 COLEC10 TMEM107 SIM1 OSGEP XRCC2 FANCM SKI PIGV SKIV2L YWHAE CDK10 SH2B1 STAMBP ZIC1 ZIC2 ZIC3 EPG5 PPP1CB CASK NBAS PACS1 PPP2CA PPP2R1A SETD2 VAC14 PIEZO2 BCL11B PPP2R5D PPP3CA NSMF SPINT2 FAM111A SEC24C COX1 COX2 UBE2T COX3 ARVCF KLF13 WDR11 MTOR CDK13 CSNK2A1 IGHM TTC37 ND1 SETBP1 ND4 MRPS14 ND5 ND6 DCHS1 NUP133 PTCH2 PTRH2 ANKRD11 AUTS2 B9D1 MPLKIP PRKAR1A KBTBD13 FLCN NKX2-5 FOXP1 TRNF CTBP1 SMO SMS TRNH FUCA1 IGLL1 TRNL1 PRKG1 NGLY1 SLC45A1 CTNND1 TBR1 TRNQ CTNND2 TRNS1 TRNS2 TRNW SUFU MAP2K1 ERMARD MAP2K2 FZD2 MCTP2 TRIM37 SIX2 SLX4 MUSK AFF4 RAI1 SEMA3E SOS1 PHACTR1 SOS2 IL11RA SOX9 ATP6V1A TCTN3 MYH3 ATP6V1B2 KIF1BP INTU MASP1 ATP6V1E1 ZMYND11 MYH11 EED DDX59 EMC1 GPAA1 MYLK WDR4 ATRX CHST14 TMEM237 AVP TMEM94 MYOD1 INPPL1 IQSEC2 RNF113A KIAA0586 INSR HDAC8 PTDSS1 CPLX1 NKX3-2 GATA6 GBA SPART FGFRL1 NFASC NKX2-6 QRICH1 PSMD12 ITGA3 NEB PTCH1 C12ORF57 PTEN NSUN2 CCNK DPM1 AHDC1 ZEB2 ZBTB24 PTH1R PHGDH FREM1 B3GAT3 FGF17 STAT3 MKS1 BGN KIAA0753 RUSC2 XYLT2 GJA1 BMP2 FREM2 SEC24D FAM20C BMPR1A ANOS1 PTPN11 GK KISS1R TXNL4A NF1 CEP120 GPC3 BRCA1 GLB1 BRAF BRCA2 PROKR2 KLHL7 FIG4 WASHC5 FGF20 CCDC47 KCNH1 GLE1 KCNJ2 NFIX GLI3 DHCR7 BRPF1 MYPN BUB1B ABCD4 PEX2 PEX5 SMG9 PYCR1 ALDH18A1 PACS2 KIAA0556 CACNA1G TAC3 DLX4 TACR3 TAF1 BMPER HERC1 CAMTA1 TMEM231 CPLANE1 MAP3K7 MAPRE2 KISS1 GNRH1 GNRHR PHIP MED12 TRAPPC9 PIGO TBX1 ALG1 NOTCH2 NOTCH3 TBCD TBCE KNL1 GP1BB DNMT3B TBX2 RAD51 RAD51C TBX15 KRAS SLC12A6 MARS2 RAF1 RPGRIP1 DPH1 AKT3 FAT4 TCF3 SOST B3GLCT RAPSN TCF12 RPGRIP1L NRAS SRD5A3 RASA2 NUP107 USB1 GNE RB1 TCOF1 EBF3 SLC26A2 CAMK2A SMCHD1 DOK7 UBE3B DUSP6 ROR2 DDR2 TPRKB DVL1 NUP88 DVL3 NSD1 LMBR1 ABCC9 TWIST2 SEMA5A SALL4 FANCL RIPK4 SPECC1L DPF2 LBR RET SIK3 RUNX2 MED13L CBL SHOC2 TBL1XR1 NXN CIT TFAP2A ANKH TFAP2B DICER1 JMJD1C WDPCP PALB2 LETM1 PDHX RSPRY1 RFWD3 POLR3A KIF7 ADGRG6 CEP55 CCND2 ESCO2 RIT1 TTC7A GRIP1 TGFB2 TGFB3 IL1RAPL1 TGFBR1 RMRP TGFBR2 B9D2 POLR1D MFAP5 LIG4 LRPPRC GTF2E2 AP4S1 SH3PXD2B EFNB1 THRA HMGA2 ALX1 LMNA MEGF8 CDCA7 CCBE1 LOX FANCI ASXL3 ALG9 PAFAH1B1 SPRY4 TGDS RLIM MED25 LRP2 EHMT1 FIBP LRP4 LRRC8A LRP5 SPRED1 CD79A CD79B WDR73 ASXL2 PAX3 ELN SUZ12 HBA1 HBA2 KAT6B CDC42 CDH1 CSPP1 RPL5 CDH11 MAN1B1 SMAD3 SMAD4 ATP6V0A2 TCTN2 ALG13 HELLS MAF